{"id":"https://openalex.org/W4415731582","doi":"https://doi.org/10.1186/s12859-025-06290-2","title":"ESAE-SDA: ensemble sparse autoencoder framework for epigenomics-informed snoRNA-disease associations prediction","display_name":"ESAE-SDA: ensemble sparse autoencoder framework for epigenomics-informed snoRNA-disease associations prediction","publication_year":2025,"publication_date":"2025-10-31","ids":{"openalex":"https://openalex.org/W4415731582","doi":"https://doi.org/10.1186/s12859-025-06290-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/41174471"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06290-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06290-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06290-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06290-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048843617","display_name":"Xinqing Jiang","orcid":"https://orcid.org/0000-0003-0773-523X"},"institutions":[{"id":"https://openalex.org/I4210088331","display_name":"Quzhou City People's Hospital","ror":"https://ror.org/004qehs09","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210088331"]},{"id":"https://openalex.org/I4210123686","display_name":"Quzhou University","ror":"https://ror.org/024nfx323","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210123686"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinqing Jiang","raw_affiliation_strings":["Jinhua Graduate Joint Training Base, Zhejiang Chinese Medical University, Quzhou People's Hospital, Quzhou, 324000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jinhua Graduate Joint Training Base, Zhejiang Chinese Medical University, Quzhou People's Hospital, Quzhou, 324000, China","institution_ids":["https://openalex.org/I4210088331","https://openalex.org/I4210123686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100369444","display_name":"Xiaojun Chen","orcid":"https://orcid.org/0000-0002-6374-810X"},"institutions":[{"id":"https://openalex.org/I4210088331","display_name":"Quzhou City People's Hospital","ror":"https://ror.org/004qehs09","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210088331"]},{"id":"https://openalex.org/I4210123686","display_name":"Quzhou University","ror":"https://ror.org/024nfx323","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210123686"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaojun Chen","raw_affiliation_strings":["Department of Endocrine and Metabolic Disease, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, 324000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Endocrine and Metabolic Disease, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, 324000, China","institution_ids":["https://openalex.org/I4210088331","https://openalex.org/I4210123686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087391805","display_name":"Ling Xu","orcid":"https://orcid.org/0000-0001-7974-3541"},"institutions":[{"id":"https://openalex.org/I4210088331","display_name":"Quzhou City People's Hospital","ror":"https://ror.org/004qehs09","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210088331"]},{"id":"https://openalex.org/I4210123686","display_name":"Quzhou University","ror":"https://ror.org/024nfx323","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210123686"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lifeng Xu","raw_affiliation_strings":["Jinhua Graduate Joint Training Base, Zhejiang Chinese Medical University, Quzhou People's Hospital, Quzhou, 324000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jinhua Graduate Joint Training Base, Zhejiang Chinese Medical University, Quzhou People's Hospital, Quzhou, 324000, China","institution_ids":["https://openalex.org/I4210088331","https://openalex.org/I4210123686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100401274","display_name":"Feng Zhang","orcid":"https://orcid.org/0000-0002-6751-0377"},"institutions":[{"id":"https://openalex.org/I4210088331","display_name":"Quzhou City People's Hospital","ror":"https://ror.org/004qehs09","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210088331"]},{"id":"https://openalex.org/I4210123686","display_name":"Quzhou University","ror":"https://ror.org/024nfx323","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210123686"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Feng Zhang","raw_affiliation_strings":["Department of Respiratory and Critical Care, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, 324000, China. fengzhang@wmu.edu.cn","Department of Respiratory and Critical Care, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, 324000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Respiratory and Critical Care, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, 324000, China. fengzhang@wmu.edu.cn","institution_ids":["https://openalex.org/I4210123686"]},{"raw_affiliation_string":"Department of Respiratory and Critical Care, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou, 324000, China","institution_ids":["https://openalex.org/I4210088331","https://openalex.org/I4210123686"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Jiawei Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I27781120","display_name":"Wenzhou Medical University","ror":"https://ror.org/00rd5t069","country_code":"CN","type":"education","lineage":["https://openalex.org/I27781120"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiawei Chen","raw_affiliation_strings":["Ophthalmology Department, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ophthalmology Department, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China","institution_ids":["https://openalex.org/I27781120"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079358399","display_name":"Wenqian Zhang","orcid":"https://orcid.org/0000-0001-9865-6275"},"institutions":[{"id":"https://openalex.org/I4210164898","display_name":"Beijing Chaoyang Emergency Medical Center","ror":"https://ror.org/05anb7a53","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210164898"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wenqian Zhang","raw_affiliation_strings":["Department of Thoracic Surgery, Beijing Chaoyang Hospital, Capital Medical University, 8th Gongtinanlu Rd, Chaoyang District, Beijing, 100020, China. wenqian.zhang@hotmail.com","Department of Thoracic Surgery, Beijing Chaoyang Hospital, Capital Medical University, 8th Gongtinanlu Rd, Chaoyang District, Beijing, 100020, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Thoracic Surgery, Beijing Chaoyang Hospital, Capital Medical University, 8th Gongtinanlu Rd, Chaoyang District, Beijing, 100020, China. wenqian.zhang@hotmail.com","institution_ids":["https://openalex.org/I4210164898"]},{"raw_affiliation_string":"Department of Thoracic Surgery, Beijing Chaoyang Hospital, Capital Medical University, 8th Gongtinanlu Rd, Chaoyang District, Beijing, 100020, China","institution_ids":["https://openalex.org/I4210164898"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5079358399","https://openalex.org/A5100401274"],"corresponding_institution_ids":["https://openalex.org/I4210088331","https://openalex.org/I4210123686","https://openalex.org/I4210164898"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.4217,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.64465485,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"26","issue":"1","first_page":"270","last_page":"270"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9241999983787537,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9241999983787537,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.01209999993443489,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.010499999858438969,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.6564000248908997},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.60589998960495},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5181999802589417},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5120000243186951},{"id":"https://openalex.org/keywords/small-nucleolar-rna","display_name":"Small nucleolar RNA","score":0.4952000081539154},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.42289999127388},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"Ensemble learning","score":0.3961000144481659},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.38670000433921814}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.6564000248908997},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6377999782562256},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6326000094413757},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.60589998960495},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5385000109672546},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5181999802589417},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5120000243186951},{"id":"https://openalex.org/C179255354","wikidata":"https://www.wikidata.org/wiki/Q284416","display_name":"Small nucleolar RNA","level":5,"score":0.4952000081539154},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48399999737739563},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.42289999127388},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.3961000144481659},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.38670000433921814},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.38109999895095825},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.35929998755455017},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.34880000352859497},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.34389999508857727},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.29980000853538513},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2969000041484833},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29269999265670776},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.288100004196167},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.2558000087738037},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.25440001487731934},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.25360000133514404}],"mesh":[{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D020537","descriptor_name":"RNA, Small Nucleolar","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06290-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06290-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06290-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41174471","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41174471","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:4a1813752009454491f25e2b31390236","is_oa":true,"landing_page_url":"https://doaj.org/article/4a1813752009454491f25e2b31390236","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-18 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11386418","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12577141","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06290-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06290-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06290-2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4415731582.pdf","grobid_xml":"https://content.openalex.org/works/W4415731582.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1039284560","https://openalex.org/W1992208280","https://openalex.org/W2070777085","https://openalex.org/W2120920586","https://openalex.org/W2353267094","https://openalex.org/W2771031897","https://openalex.org/W2892502396","https://openalex.org/W2895679848","https://openalex.org/W3000082418","https://openalex.org/W3010127844","https://openalex.org/W3049654296","https://openalex.org/W3170286690","https://openalex.org/W3193389962","https://openalex.org/W3196927126","https://openalex.org/W4280506442","https://openalex.org/W4294811162","https://openalex.org/W4297891375","https://openalex.org/W4307178567","https://openalex.org/W4307440230","https://openalex.org/W4323653169","https://openalex.org/W4323974793","https://openalex.org/W4380986271","https://openalex.org/W4383198266","https://openalex.org/W4389918314","https://openalex.org/W4390415056","https://openalex.org/W4390563851","https://openalex.org/W4391962767","https://openalex.org/W4392061709","https://openalex.org/W4392571650","https://openalex.org/W4392791245","https://openalex.org/W4394749617","https://openalex.org/W4394858080","https://openalex.org/W4394997844","https://openalex.org/W4395015247","https://openalex.org/W4396757514","https://openalex.org/W4400362549","https://openalex.org/W4400522271","https://openalex.org/W4400875898","https://openalex.org/W4402035908","https://openalex.org/W4403218259","https://openalex.org/W4403916918","https://openalex.org/W4404628128","https://openalex.org/W4406024492","https://openalex.org/W4407605420","https://openalex.org/W4408336523","https://openalex.org/W4408771091","https://openalex.org/W4409346604","https://openalex.org/W4410800752","https://openalex.org/W4411032945","https://openalex.org/W4411497393","https://openalex.org/W4411497628","https://openalex.org/W4412680077"],"related_works":[],"abstract_inverted_index":{"Small":[0],"nucleolar":[1],"RNAs":[2,8],"(snoRNAs),":[3],"a":[4,114,128,148,186,198],"class":[5],"of":[6,21,62],"non-coding":[7],"broadly":[9],"distributed":[10],"in":[11,18,48,74,222],"eukaryotes,":[12],"are":[13,94,164],"emerging":[14],"as":[15,100],"pivotal":[16],"regulators":[17],"the":[19,205],"field":[20],"epigenomics.":[22],"In":[23],"addition":[24],"to":[25,35,141,155,208],"guiding":[26],"2'-O-methylation":[27],"and":[28,39,56,77,81,103,146,171,182,216,226],"pseudouridylation":[29],"modifications":[30],"at":[31],"specific":[32],"rRNA":[33],"sites":[34],"maintain":[36],"ribosomal":[37],"stability":[38],"support":[40],"protein":[41],"synthesis,":[42],"snoRNAs":[43,212],"have":[44,89],"been":[45],"increasingly":[46],"implicated":[47],"epigenetic":[49],"regulation,":[50],"influencing":[51],"gene":[52],"expression,":[53],"chromatin":[54],"architecture,":[55],"RNA":[57],"modification":[58],"patterns.":[59],"Accurate":[60],"identification":[61],"potential":[63,214],"snoRNA-disease":[64,130],"associations":[65],"(SDAs)":[66],"is":[67,174],"therefore":[68],"essential":[69],"for":[70],"understanding":[71],"epigenomic":[72],"dysregulation":[73],"complex":[75],"diseases":[76,203],"facilitating":[78],"early":[79],"intervention":[80],"drug":[82],"repurposing.":[83],"Although":[84],"artificial":[85],"intelligence":[86],"(AI)":[87],"methods":[88],"advanced":[90],"SDA":[91,188],"prediction,":[92],"they":[93],"still":[95],"hindered":[96],"by":[97],"issues":[98],"such":[99],"sample":[101],"imbalance":[102],"high":[104],"false-negative":[105],"rates.":[106],"To":[107],"address":[108],"these":[109],"challenges,":[110],"we":[111],"propose":[112],"ESAE-SDA,":[113],"novel":[115],"model":[116],"integrating":[117],"sparse":[118,150],"autoencoders":[119],"with":[120,152,213],"an":[121],"ensemble":[122,172],"learning":[123],"framework.":[124],"ESAE-SDA":[125,192],"first":[126],"constructs":[127],"comprehensive":[129],"representation":[131],"using":[132],"multi-source":[133],"similarity":[134],"metrics.":[135],"It":[136],"then":[137],"applies":[138],"k-means":[139],"clustering":[140],"select":[142],"high-confidence":[143],"negative":[144],"samples":[145],"employs":[147],"deep":[149],"autoencoder":[151],"sparsity":[153],"constraints":[154],"learn":[156],"compact,":[157],"discriminative":[158],"embeddings.":[159],"Finally,":[160],"multiple":[161],"GNN-based":[162],"learners":[163],"independently":[165],"trained":[166],"on":[167,185,201],"dynamically":[168],"resampled":[169],"data,":[170],"inference":[173],"performed":[175],"via":[176],"weighted":[177],"fusion,":[178],"substantially":[179],"enhancing":[180],"robustness":[181],"generalization.":[183],"Experiments":[184],"public":[187],"dataset":[189],"demonstrate":[190],"that":[191],"consistently":[193],"outperforms":[194],"state-of-the-art":[195],"methods.":[196],"Notably,":[197],"case":[199],"study":[200],"ophthalmic":[202],"highlights":[204],"model's":[206],"ability":[207],"uncover":[209],"epigenetically":[210],"relevant":[211],"regulatory":[215],"therapeutic":[217],"significance,":[218],"underscoring":[219],"its":[220],"value":[221],"epigenomics-driven":[223],"disease":[224],"research":[225],"target":[227],"discovery.":[228]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-31T00:00:00"}
